Here we show the code to reproduce the analyses of: Risso and Pagnotta (2019). Within-sample standardization and asymmetric winsorization lead to accurate classification of RNA-seq expression profiles. In preparation.
This file belongs to the repository: https://github.com/drisso/awst_analysis.
The code is released with license GPL v3.0.
awstif (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("drisso/awst")
The collection of the SEQC datasets is available throught the seqc Bioconductor package. It can be installed with the following.
BiocManager::install("seqc")
We next build the data matrix from the “ILM_aceview” experiments. We remove duplicate gene symbols, ERCC spike-ins, and genes with no ENTREZ ID.
| AGR | BGI | CNL | COH | MAY | NVS | Sum | |
|---|---|---|---|---|---|---|---|
| A | 4 | 5 | 5 | 4 | 5 | 4 | 27 |
| B | 4 | 5 | 5 | 4 | 5 | 4 | 27 |
| C | 4 | 5 | 5 | 4 | 5 | 4 | 27 |
| D | 4 | 5 | 5 | 4 | 5 | 4 | 27 |
| Sum | 16 | 20 | 20 | 16 | 20 | 16 | 108 |
## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] awst_0.0.3 dendextend_1.12.0 cluster_2.1.0 knitr_1.25
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.2 pillar_1.4.2 compiler_3.6.1
## [4] highr_0.8 viridis_0.5.1 tools_3.6.1
## [7] digest_0.6.21 evaluate_0.14 tibble_2.1.3
## [10] gtable_0.3.0 viridisLite_0.3.0 pkgconfig_2.0.3
## [13] rlang_0.4.0 yaml_2.2.0 xfun_0.10
## [16] gridExtra_2.3 stringr_1.4.0 dplyr_0.8.3
## [19] grid_3.6.1 tidyselect_0.2.5 glue_1.3.1
## [22] R6_2.4.0 rmarkdown_1.16 ggplot2_3.2.1
## [25] purrr_0.3.2 magrittr_1.5 scales_1.0.0
## [28] htmltools_0.4.0 assertthat_0.2.1 colorspace_1.4-1
## [31] stringi_1.4.3 lazyeval_0.2.2 munsell_0.5.0
## [34] crayon_1.3.4